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MIMM 324 > 2. The Baltimore Scheme > Flashcards

2. The Baltimore Scheme Flashcards

1
Q

what information is encoded in a viral genome? (5)

A

gene products to complete its life cycle:
1. replication of viral genome
2. assembly and packaging of genome
3. regulation and timing of replication cycle
4. modulation of host defenses
5. spread to other cells

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2
Q

what is the main principle of the baltimore scheme?

A

viral genomes MUST make mRNA to be read by host ribosomes

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3
Q

what does positive polarity of a DNA or RNA strand mean?

A

coding strand

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4
Q

what does negative polarity of a DNA or RNA strand mean?

A

non-coding/template/complementary

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5
Q

describe the polarity of mRNA

A

POSITIVE –> bc ready to be read by ribosomes

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6
Q

are all positive RNAs mRNA?

A

NO –> not all are translated

ex. genomic RNA

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7
Q

why is + RNA in retroviruses not mRNA?

A

retroviruses are + RNA viruses that use RT to make DNA that integrates into the host to make mRNA

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8
Q

What are the 7 types of viruses in the baltimore scheme?

A
  1. dsDNA
  2. ssDNA
  3. dsRNA
  4. (+) ssRNA
  5. (-) ssRNA
  6. (+) ssRNA-RT
  7. dsDNA-RT
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9
Q
  1. describe dsDNA viruses
A

dsDNA is copied by DNA polymerases and mRNA is made directly

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10
Q

what are the 2 types of dsDNA viruses?

A
  1. genomes copied by host DNA polymerase
  2. genomes that encode their own DNA polymerase
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11
Q
  1. describe ssDNA genomes
A

genome is circular or linear

(+) or (-) converted to dsDNA with DNA polymerase to produce mRNA with host transcription machinery

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12
Q

why do RNA viruses replicate in the cytoplasm?

A

they cannot use the host RNA polymerase to make mRNA bc it uses DNA as a template –> requires its own polymerase to make mRNA from RNA

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13
Q

which types of viruses use RdRP? how does RdRP work?

A

dsRNA, (+) RNA, and (-) RNA viruses encode RdRP to make RNA and mRNA from RNA

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14
Q

which types of viruses use RT? how does RT work?

A

ssRNA-RT and dsDNA-RT viruses encode RT to make DNA tha is transcribed by the host RNA pol II to make mRNA

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15
Q
  1. describe dsRNA genomes
A

dsRNA must be copied to mRNA using RdRP* bc ribosomes can’t translate dsRNA

*viruses carry RdRP in the viral particle

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16
Q
  1. describe (+) ssRNA genomes
A

directly translated –> doesn’t need to carry RdRP in the particle bc RNA can be translated in the host to make RdRP and make MORE (+) ssRNA

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17
Q
  1. describe (-) ssRNA genomes
A

cannot be translated so must carry RdRP to make mRNA

18
Q
  1. describe (+) ssRNA-RT genomes
A

it is positive but cannot be translated so must be copied by RT* to (-) ssDNA then to dsDNA –> dsDNA integrates into the host DNA (PROVIRUS) by integrase to be transcribed by host RNA pol to make mRNA

*RT is carried in the viral particle

19
Q
  1. describe dsDNA-RT genomes
A

the dsDNA is gapped (cannot be copied to mRNA) –> converted to full dsDNA then mRNA

the +RNA is then converted to -DNA to remake gapped dsDNA by RT

20
Q

what happens when multiple viruses co-infect the same cell?

A

viral genome segments undergo REASSORTMENT –> genomes get mixed up during replication to cause rapid gain in evolution

21
Q

why are lab animals good?

A

to study pathogenesis

22
Q

how were viruses propagated before cell culture? how does this work?

A

in embryonated chicken eggs
- 5-14 days after fertilization a hole is drilled in the shell and virus is injected –> to make vaccine

23
Q

what was the first virus they found could multiply in cultured cells?

A

poliovirus

24
Q

what are the 2 types of cell culture?

A
  1. primary cell culture –> prepared from animal tissues, limited life span
  2. continuous cell culture –> single cell type that propagates indefinitely
25
Q

what is the benefit of using primary cell cultures?

A

more biologically accurate –> these are the actual cell types being infected by the virus

26
Q

example of continuous cell lines

A

HeLa cells –> tumour tissue

27
Q

what is the downside of using continuous cell lines?

A

may not resemble cell of origin

28
Q

what are cytopathic effects? and some examples?

A

CPE are evidence of viral growth in cultured cells

ex. detachment, lysis, syncytium formation (cell fusion), nuclear shrinking/swelling, accumulation of virions/viral proteins, altered membrane

29
Q

describe the PLAQUE ASSAY
- what does it assume?

A

to quantify the number of infectious particles –> as PFU
assumes 1 viral particle produces a plaque –> 1 cell is infected and lysed, then neighbouring cells get infected to form a plaque

30
Q

what is virus titer?

A

concentration of a virus in a sample

31
Q

how do you calculate the virus titer?

A

find titer of 10^(-6) dilution –> #PFU/vol
ex. 17 PFU/0.1ml = 170 PFU/ml

then, find titer of undiluted stock –> dilution titerdilution
ex. 170 PFU/ml10^6 = 1.7x10^8 PFU/ml

32
Q

describe the FOCUS-FORMING UNIT ASSAY

A

to find # of infectious particles for viruses that don’t lyse cells (i.e. don’t create plaques)

after infection, cells are permeabilized and stained with antibody against viral protein

33
Q

what is the particle-to-PFU ratio? why do we use it?

A

of actual viral particles / # of infectious particles(PFU)

we use this because not all particles can cause infection

34
Q

what would cause a viral particle to not be able to initiate an infection?

A

damaged, mutations, “empty”, complexity of life cycle, anti-viral defense, missing part of genome

35
Q

what is the multiplicity of infection (MOI)?

A

average number of infectious particles ADDED per cell

(**not the same as # of infectious particles a cell receives)

36
Q

how do you calculate MOI?

A

EX. add 10^7 PFUs to 10^6 cells –> 10 particles/cell ADDED –> MOI = 10

37
Q

What does MOI = 10 indicate?

A

each cell does NOT receive 10 virions –> infection is due to random collisions so some cells be uninfected and some can receive diff numbers of particles

38
Q

describe the distribution of virus particles per cell

A

poisson distribution

39
Q

what happens if you use a low MOI

A

viruses < cells
- allows you to have multiple cycles of infection

40
Q

what happens if you use an optimal MOI

A

viruses ~ cells
- have most cells infected

41
Q

what happens if you use a high MOI?

A

viruses > cells
- when every cell needs to be infected

MIMM 324 (37 decks)

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